Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

Phosphate (P) is a crucial macronutrient for normal plant growth and development. The P availability in soils is a limitation factor, and understanding genetic factors playing roles in plant adaptation for improving P uptake is of great biological importance. Genome-wide association studies (GWAS) have become indispensable tools in unraveling the genetic basis of complex traits in various plant species. In this study, a comprehensive GWAS was conducted on diverse tomato (Solanum lycopersicum L.) accessions grown under normal and low P conditions for two weeks. Plant traits such as shoot height, primary root length, plant biomass, shoot inorganic content (SiP), and root inorganic content (RiP) were measured. Among several models of GWAS tested, the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) models were used for the identification of single nucleotide polymorphisms (SNPs). Among all the traits analyzed, significantly associated SNPs were recorded for PB, i.e., 1 SNP (SSL4.0CH10_49261145) under control P, SiP, i.e., 1 SNP (SSL4.0CH08_58433186) under control P and 1 SNP (SSL4.0CH08_51271168) under low P and RiP i.e., 2 SNPs (SSL4.0CH04_37267952 and SSL4.0CH09_4609062) under control P and 1 SNP (SSL4.0CH09_3930922) under low P condition. The identified SNPs served as genetic markers pinpointing regions of the tomato genome linked to P-responsive traits. The novel candidate genes associated with the identified SNPs were further analyzed for their protein-protein interactions using STRING. The study provided novel candidate genes, viz. Solyc10g050370 for PB under control, Solyc08g062490, and Solyc08g062500 for SiP and Solyc09g010450, Solyc09g010460, Solyc09g010690, and Solyc09g010710 for RiP under low P condition. These findings offer a glimpse into the genetic diversity of tomato accessions' responses to P uptake, highlighting the potential for tailored breeding programs to develop P-efficient tomato varieties that could adapt to varying soil conditions, making them crucial for sustainable agriculture and addressing global challenges, such as soil depletion and food security.

Paclobutrazol improves surface water use efficiency by regulating allometric trait behavior in maize

Paclobutrazol (PBZ) role in drought management of maize is least understood. In maize, root traits are linked with surface water management. Over three years, early and terminal deficit irrigation (EDI and TDI) with or without PBZ were imposed on DKC-9144 and PG-2475 maize varieties. Several allometric parameters viz. stem height, stem diameter, leaf area and root traits along with physiological processes were measured. Implication of these parameters in the management of soil surface irrigation in terms of water use efficiency (WUE) was demonstrated in maize. Increased number of lateral roots and root number density in DKC-9144 provided more surface area for water absorption for better management of EDI. Root growth rates showed a similar pattern with root length, root surface areas, and root numbers in EDI. Elevated expressions of ZmRTCL, ZmRTCS and ZmARF34 in EDI and EDI plus PBZ were associated with seminal roots and root laterals initiation. Under TDI alone or in combination with PBZ, root lengths (BRL, CRL, SRL) and root surface areas varied in DKC-9144 and PG-2475 over control. Furthermore, correlation analysis showed that decrease in WUE under TDI was significantly associated with a reduction in stem thickness and leaf surface area. For WUE_N in TDI and PBZ plus TDI, structural equation modelling proposed, brace root surface area (BRSA_N) as a positive contributor, while a negative contributor was seminal root surface area (SRSA_N). Present study explained the importance of specific root traits and their association with other allometric parameters for improving WUE in DKC-9144 variety of maize and the crop in general.

Recent trends in root phenomics of plant systems with available methods- discrepancies and consonances

The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.

Green synthesis of zinc oxide nanoparticles using Eucalyptus lanceolata leaf litter: characterization, antimicrobial and agricultural efficacy in maize

In the present study, green synthesis of zinc oxide nanoparticles (ZnO NP) using Eucalyptus lanceolatus (leaf litter) extract was explored after characterization with UV spectrophotometery, Fourier Transform Infrared analysis, X-ray diffraction and TEM studies. ZnO NPs stability was ensured with - 32.1 mV zeta potential, while TEM showed ZnO NP as hexagonal structure (100 nm). In vitro antimicrobial activity showed potential of ZnO NP against pathogens causing diseases in maize plants. Both in vitro and in vivo studies of ZnO NP and ZnSO₄ (200 ppm and 400 ppm) over a two year period (2019, 2020) were conducted on Zea mays L. var. PG2458. ZnO NP seed priming improved seed vigor index, germination percentage, shoot and root length and fresh biomass. Foliar application improved stem diameter and leaf surface area. Physiological status was relatively better, while reproductive attributes got altered to guide resource allocation for better cob growth and biomass with ZnO NP. Leaf, cob, grain and total Zn was maximum for 200 ppm ZnO NP. Translocation of Zn from leaf to cob and cob to grain was faster for ZnO NP compared to ZnSO₄. Higher concentration (400 ppm) of ZnO NPs and ZnSO₄ proved phytotoxic for plant growth attributes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01136-0.

Post-harvest Management of Alternaria Induced Rot in Tomato Fruits With Essential Oil of Zanthoxylum armatum DC

Alternaria fruit rot is a major disease caused by Alternaria alternata (Fr.) Keissl., a prolific fungal pathogen. Among post-harvest diseases of tomato, fruit rot induced by A. alternata is the most damaging. Antifungal agents are widely used to control post-harvest management of tomato fruits. However, negative impacts of fungicidal residues in edible fruits and vegetables on human health cannot be over ruled. Eco-friendly ways of controlling Alternaria rot in tomato fruits offer a novel way of tomato rot management. The current study proposes an alternate method in controlling tomato fruit rots through Zanthoxylum armatum DC essential oil (EO) application. Gas chromatography-mass spectrometry profiling showed eucalyptol and sabinene as major components of Z. armatum EO. Furthermore, EO applied (0.5–4.5 μl/ml) showed significant inhibition of A. alternata growth (p > 0.05) at 4.5 μl concentration tested. Lipid peroxidation assays revealed significant reduction in membrane damage in tomato fruits treated by EO compared to alone inoculated fruits with A. alternata. Elevated activities of superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase coupled with enhanced antioxidants such as ascorbic acid, glutathione, proline, and total phenols in EO-treated fruits may be linked with better fruit rot management than control fruits inoculated with A. alternata-induced rot alone. Mycelia and spore production was dramatically reduced in EO applied tomato fruits over A. alternata alone in tomato fruits (p > 0.05). Interestingly, free radical scavenging activities of EO applied tomato fruits showed significant improvement compared to only pathogen-inoculated tomato fruits. Findings propose practical utility of Z. armatum EO as a plant-based antifungal for post-harvest management of Alternaria rot in tomato fruits.

Nickel excess affects phenology and reproductive attributes of Asterella wallichiana and Plagiochasma appendiculatum growing in natural habitats

Bryophytes are potent metal absorbers, thriving well on heavy metal (HM)-polluted soils. Mechanisms controlling uptake, compartmentalization and impacts of HMs on bryophytes life cycle are largely unknown. The current study is an effort to decipher mechanisms of nickel (Ni) excess-induced effects on the phenological events of two bryophytes, Asterella wallichiana and Plagiochasma apendiculatum growing in natural habitats. Observations revealed Ni-excess induced negative impacts on abundance, frequency of occurrence of reproductive organs, population viability and morphological traits, spore viability and physiological attributes of both the liverworts. Results led us conclude that P. appendiculatum survived better with the lowest impact on its life cycle events than A. wallichiana under Ni excess in natural habitats. Our findings collectively provide insights into the previously unknown mechanisms of Ni-induced responses in liverworts with respect to phenological attributes, as well as demonstrate the potential of P. appendiculatum to survive better in Ni excess habitats.